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Potassium in PDB 3w1j: Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela in Complex with Thiosulfate

Enzymatic activity of Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela in Complex with Thiosulfate

All present enzymatic activity of Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela in Complex with Thiosulfate:
2.9.1.1;

Protein crystallography data

The structure of Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela in Complex with Thiosulfate, PDB code: 3w1j was solved by Y.Itoh, S.Sekine, S.Yokoyama, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.52 / 3.25
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 92.442, 116.372, 124.788, 102.09, 93.39, 106.06
R / Rfree (%) 20 / 26.6

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela in Complex with Thiosulfate (pdb code 3w1j). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 5 binding sites of Potassium where determined in the Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela in Complex with Thiosulfate, PDB code: 3w1j:
Jump to Potassium binding site number: 1; 2; 3; 4; 5;

Potassium binding site 1 out of 5 in 3w1j

Go back to Potassium Binding Sites List in 3w1j
Potassium binding site 1 out of 5 in the Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela in Complex with Thiosulfate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela in Complex with Thiosulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K2001

b:0.2
occ:1.00
 OD1 A:ASP317 2.5 0.3 1.0
OD2 B:ASP317 3.0 90.6 1.0
OD1 A:ASN140 3.2 83.9 1.0
OD1 B:ASN140 3.5 78.5 1.0
CG A:ASP317 3.7 0.9 1.0
CG B:ASP317 3.7 88.6 1.0
CB B:ASP317 3.9 85.8 1.0
OG1 A:THR320 3.9 82.8 1.0
N A:ASP317 4.1 83.5 1.0
CG A:ASN140 4.2 77.6 1.0
CB A:ASP317 4.3 0.7 1.0
N B:ASP317 4.4 75.1 1.0
CG B:ASN140 4.4 72.8 1.0
CG2 A:THR320 4.6 80.1 1.0
O A:ASN140 4.6 74.9 1.0
CA A:ILE316 4.6 79.5 1.0
OD2 A:ASP317 4.6 0.5 1.0
CA A:ASN140 4.7 68.3 1.0
CA B:ASP317 4.7 77.3 1.0
CB A:ASN140 4.8 72.0 1.0
OD1 B:ASP317 4.8 87.4 1.0
CA A:ASP317 4.9 87.9 1.0
CB A:THR320 4.9 80.4 1.0
C A:ILE316 4.9 80.1 1.0
O A:GLN291 4.9 73.6 1.0
CD A:GLN291 4.9 70.4 1.0
NE2 A:GLN291 4.9 84.0 1.0
OG1 B:THR320 4.9 64.2 1.0

Potassium binding site 2 out of 5 in 3w1j

Go back to Potassium Binding Sites List in 3w1j
Potassium binding site 2 out of 5 in the Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela in Complex with Thiosulfate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela in Complex with Thiosulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K501

b:0.7
occ:1.00
 OD1 D:ASN140 3.0 94.4 1.0
OD1 C:ASN140 3.7 0.6 1.0
OD2 D:ASP317 3.7 0.8 1.0
OG1 D:THR320 3.9 93.0 1.0
CG D:ASN140 3.9 88.4 1.0
OD2 C:ASP317 4.0 0.7 1.0
CB C:ASP317 4.0 0.1 1.0
CG2 D:THR320 4.1 98.6 1.0
CG D:ASP317 4.1 0.0 1.0
O D:ASN140 4.1 88.3 1.0
NE2 D:GLN291 4.2 0.0 1.0
N D:ASP317 4.2 90.9 1.0
CG C:ASP317 4.2 0.7 1.0
CB D:ASN140 4.2 77.3 1.0
CA D:ASN140 4.3 79.1 1.0
OD1 D:ASP317 4.4 0.2 1.0
CA D:ILE316 4.4 90.3 1.0
CG C:ASN140 4.4 92.7 1.0
CB D:THR320 4.5 95.8 1.0
O D:GLN291 4.6 97.9 1.0
C D:ASN140 4.7 87.6 1.0
N C:ASP317 4.7 0.6 1.0
CB D:ILE316 4.8 88.1 1.0
ND2 C:ASN140 4.9 87.6 1.0
C D:ILE316 4.9 88.7 1.0
CB D:ASP317 4.9 0.3 1.0
CD D:GLN291 5.0 0.3 1.0
CA C:ASP317 5.0 0.1 1.0

Potassium binding site 3 out of 5 in 3w1j

Go back to Potassium Binding Sites List in 3w1j
Potassium binding site 3 out of 5 in the Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela in Complex with Thiosulfate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela in Complex with Thiosulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K501

b:0.9
occ:1.00
 OD1 E:ASN140 3.2 88.5 1.0
OD2 E:ASP317 3.2 0.2 1.0
OD1 F:ASN140 3.5 0.7 1.0
OD2 F:ASP317 3.6 0.4 1.0
OG1 E:THR320 3.8 0.1 1.0
N E:ASP317 3.9 0.9 1.0
CG F:ASP317 4.1 0.6 1.0
CG E:ASN140 4.1 89.2 1.0
CB F:ASP317 4.2 0.3 1.0
CG F:ASN140 4.2 0.2 1.0
CG E:ASP317 4.3 0.2 1.0
CA E:ILE316 4.3 0.2 1.0
CA E:ASN140 4.3 84.1 1.0
CB E:ASN140 4.3 80.6 1.0
CG2 E:THR320 4.3 0.8 1.0
O E:ASN140 4.4 89.0 1.0
CB E:ASP317 4.5 0.7 1.0
C E:ILE316 4.6 98.9 1.0
CB E:ILE316 4.6 0.5 1.0
CB E:THR320 4.7 0.6 1.0
ND2 F:ASN140 4.7 0.1 1.0
N F:ASP317 4.7 0.5 1.0
C E:ASN140 4.8 86.1 1.0
CA E:ASP317 4.8 0.3 1.0
CG2 E:ILE316 4.9 0.6 1.0
O E:GLN291 4.9 0.9 1.0
NE2 E:GLN291 5.0 0.7 1.0

Potassium binding site 4 out of 5 in 3w1j

Go back to Potassium Binding Sites List in 3w1j
Potassium binding site 4 out of 5 in the Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela in Complex with Thiosulfate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela in Complex with Thiosulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
G:K501

b:0.2
occ:1.00
 OD1 H:ASN140 3.3 0.7 1.0
OD2 H:ASP317 3.3 0.5 1.0
OD2 G:ASP317 3.4 0.1 1.0
OD1 G:ASN140 3.5 0.0 1.0
N H:ASP317 4.0 0.8 1.0
CG H:ASN140 4.0 0.7 1.0
CB H:ASN140 4.0 0.5 1.0
CA H:ASN140 4.1 0.0 1.0
CG G:ASN140 4.2 91.0 1.0
OG1 H:THR320 4.2 0.8 1.0
CG H:ASP317 4.2 0.9 1.0
CG G:ASP317 4.3 0.9 1.0
CB H:ASP317 4.3 0.9 1.0
CA H:ILE316 4.4 0.0 1.0
O H:ASN140 4.4 0.0 1.0
CG2 H:THR320 4.4 0.0 1.0
CB G:ASP317 4.5 0.7 1.0
C H:ASN140 4.7 0.3 1.0
C H:ILE316 4.7 1.0 1.0
CA H:ASP317 4.8 0.8 1.0
CB G:ASN140 4.9 84.0 1.0
N G:ASP317 4.9 0.2 1.0
O H:GLN291 4.9 0.6 1.0
ND2 G:ASN140 4.9 86.5 1.0
CB H:THR320 4.9 0.9 1.0
CB H:ILE316 5.0 0.3 1.0

Potassium binding site 5 out of 5 in 3w1j

Go back to Potassium Binding Sites List in 3w1j
Potassium binding site 5 out of 5 in the Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela in Complex with Thiosulfate


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Crystal Structure of the N-Terminal Truncated Selenocysteine Synthase Sela in Complex with Thiosulfate within 5.0Å range:
probe atom residue distance (Å) B Occ
I:K501

b:0.1
occ:1.00
 OD2 I:ASP317 3.3 95.1 1.0
OD1 J:ASN140 3.3 89.3 1.0
OD1 I:ASN140 3.4 90.3 1.0
OD2 J:ASP317 3.6 0.5 1.0
OG1 J:THR320 3.7 0.5 1.0
CG J:ASP317 3.8 0.7 1.0
N J:ASP317 3.9 96.6 1.0
CG J:ASN140 4.2 78.4 1.0
OD1 J:ASP317 4.2 0.4 1.0
CA J:ILE316 4.3 83.2 1.0
CG I:ASP317 4.3 93.9 1.0
CB J:ASP317 4.3 0.2 1.0
CG I:ASN140 4.4 82.8 1.0
CA J:ASN140 4.4 59.9 1.0
O J:ASN140 4.4 69.0 1.0
CB I:ASP317 4.4 93.1 1.0
CB J:ASN140 4.5 67.9 1.0
CG2 J:THR320 4.6 0.2 1.0
C J:ILE316 4.6 91.7 1.0
O J:ARG315 4.7 85.7 1.0
CB J:THR320 4.7 0.9 1.0
CA J:ASP317 4.7 0.8 1.0
NE2 I:GLN291 4.9 93.8 1.0
CB J:ILE316 4.9 71.3 1.0
C J:ASN140 4.9 64.3 1.0
O J:GLN291 5.0 82.2 1.0
N I:ASP317 5.0 87.4 1.0

Reference:

Y.Itoh, M.J.Brocker, S.Sekine, G.Hammond, S.Suetsugu, D.Soll, S.Yokoyama. Decameric Sela-Trna(Sec) Ring Structure Reveals Mechanism of Bacterial Selenocysteine Formation Science V. 340 75 2013.
ISSN: ISSN 0036-8075
PubMed: 23559248
DOI: 10.1126/SCIENCE.1229521
Page generated: Mon Aug 12 09:50:12 2024

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